Bantu language trees reflect the spread of farming across sub-Saharan Africa: a maximum-parsimony analysis

Linguistic divergence occurs after speech communities divide, in a process similar to speciation among isolated biological populations. The resulting languages are hierarchically related, like genes or species. Phylogenetic methods developed in evolutionary biology can thus be used to infer language trees, with the caveat that 'borrowing' of linguistic elements between languages also occurs, to some degree. Maximum-parsimony trees for 75 Bantu and Bantoid African languages were constructed using 92 items of basic vocabulary. The level of character fit on the trees was high (consistency index was 0.65), indicating that a tree model fits Bantu language evolution well, at least for the basic vocabulary. The Bantu language tree reflects the spread of farming across this part of sub-Saharan Africa between ca. 3000 BC and AD 500. Modern Bantu subgroups, defined by clades on parsimony trees, mirror the earliest farming traditions both geographically and temporally. This suggests that the major subgroups of modern Bantu stem from the Neolithic and Early Iron Age, with little subsequent movement by speech communities.     

Historical linguistics as a sequence optimization problem: the evolution and biogeography of Uto‐Aztecan languages

Language origins and diversification are vital for mapping human history. Traditionally, the reconstruction of language trees has been based on cognate forms among related languages, with ancestral protolanguages inferred by individual investigators. Disagreement among competing authorities is typically extensive, without empirical grounds for resolving alternative hypotheses. Here, we apply analytical methods derived from DNA sequence optimization algorithms to Uto‐Aztecan languages, treating words as sequences of sounds. Our analysis yields novel relationships and suggests a resolution to current conflicts about the Proto‐Uto‐Aztecan homeland. The techniques used for Uto‐Aztecan are applicable to written and unwritten languages, and should enable more empirically robust hypotheses of language relationships, language histories, and linguistic evolution.     

Cladistic analysis of molecular and morphological data

Considerable progress has been made recently in phylogenetic reconstruction in a number of groups of organisms. This progress coincides with two major advances in systematics: new sources have been found for potentially informative characters (i. e., molecular data) and (more importantly) new approaches have been developed for extracting historical information from old or new characters (i. e., Hennigian phylogenetic systematics or cladistics). The basic assumptions of cladistics (the existence and splitting of lineages marked by discrete, heritable, and independent characters, transformation of which occurs at a rate slower than divergence of lineages) are discussed and defended. Molecular characters are potentially greater in quantity than (and usually independent of) more traditional morphological characters, yet their great simplicity (i. e., fewer potential character states; problems with determining homology), and difficulty of sufficient sampling (particularly from fossils) can lead to special difficulties. Expectations of the phylogenetic behavior of different types of data are investigated from a theoretical standpoint, based primarily on variation in the central parameter λ (branch length in terms of expected number of character changes per segment of a tree), which also leads to possibilities for character and character state weighting. Also considered are prospects for representing diverse yet clearly monophyletic clades in larger-scale cladistic analyses, e. g., the exemplar method vs. “compartmentalization” (a new approach involving substituting an inferred “archetype” for a large clade accepted as monophyletic based on previous analyses). It is concluded that parsimony is to be preferred for synthetic, “total evidence” analyses because it appears to be a robust method, is applicable to all types of data, and has an explicit and interpretable evolutionary basis. © 1994 Wiley-Liss, Inc.     

Mitochondrial DNA diversity in two ethnic groups in Southeastern Kenya: Perspectives from the northeastern periphery of the bantu expansion

The Bantu languages are widely distributed throughout sub‐Saharan Africa. Genetic research supports linguists and historians who argue that migration played an important role in the spread of this language family, but the genetic data also indicates a more complex process involving substantial gene flow with resident populations. In order to understand the Bantu expansion process in east Africa, mtDNA hypervariable region I variation in 352 individuals from the Taita and Mijikenda ethnic groups was analyzed, and we evaluated the interactions that took place between the Bantu‐ and non‐Bantu‐speaking populations in east Africa. The Taita and Mijikenda are Bantu‐speaking agropastoralists from southeastern Kenya, at least some of whose ancestors probably migrated into the area as part of Bantu migrations that began around 3,000 BCE. Our analyses indicate that they show some distinctive differences that reflect their unique cultural histories. The Taita are genetically more diverse than the Mijikenda with larger estimates of genetic diversity. The Taita cluster with other east African groups, having high frequencies of haplogroups from that region, while the Mijikenda have high frequencies of central African haplogroups and cluster more closely with central African Bantu‐speaking groups. The non‐Bantu speakers who lived in southeastern Kenya before Bantu speaking groups arrived were at least partially incorporated into what are now Bantu‐speaking Taita groups. In contrast, gene flow from non‐Bantu speakers into the Mijikenda was more limited. These results suggest a more complex demographic history where the nature of Bantu and non‐Bantu interactions varied throughout the area. Am J Phys Anthropol 150:482–491, 2013. © 2013 Wiley Periodicals, Inc.     

Effects of Metal Mixtures on Aquatic Biota: A Review of Observations and Methods

A brief review of the historical development of metal mixture interaction analyses is presented. The two major classifications of mixture models are outlined, the “Concentration Addition” and the “Response Addition” approaches. Within these two categories, a number of graphical, mathematical and statistical methods have been used, such as the toxic unit approach, relative potencies, toxicity equivalence factors, and dose-response relationships that have been described using several methods such as probit, logit, and regression analyses. A database was generated to evaluate the frequency of occurrence of less than additive, strictly additive, and more than additive responses to metal mixture effects reported in the literature. The three responses occurred at 43, 27, and 29%, respectively. The database is available electronically from the lead author. The research required to determine the most appropriate methods to quantify the effects of metal mixtures in an ecological risk assessment (ERA) framework is discussed. Until this research is completed, ERAs should use existing models such as the toxic unit or the effects addition approach. Bioaccumulation measurements by organisms for which the accumulation to response relationship is known would also be a useful complement.     

Post-marital residence patterns show lineage-specific evolution

Where a newly-married couple lives, termed post-marital residence, varies cross-culturally and changes over time. While many factors have been proposed as drivers of this change, among them general features of human societies like warfare, migration and gendered division of subsistence labour, little is known about whether changes in residence patterns exhibit global regularities. Here, we study ethnographic observations of post-marital residence in societies from five large language families (Austronesian, Bantu, Indo-European, Pama-Nyungan and Uto-Aztecan), encompassing 371 ethnolinguistic groups ranging widely in local ecologies and lifeways, and covering over half the world's population and geographical area. We apply Bayesian comparative methods to test the hypothesis that post-marital residence patterns have evolved in similar ways across different geographical regions. By reconstructing past post-marital residence states, we compare transition rates and models of evolution across groups, while integrating the historical descent relationships of human societies. We find that each language family possesses its own best fitting model, demonstrating that the mode and pace of post-marital residence evolution is lineage-specific rather than global.     

Cladistic analysis of languages: Indo-European classification based on lexicostatistical data

The phylogeny of the Indo‐European (IE) language family is reconstructed by application of the cladistic methodology to the lexicostatistical dataset collected by Dyen (about 200 meanings, 84 speech varieties, the Hittite language used as a functional outgroup). Three different methods of character coding provide trees that show: (a) the presence of four groups, viz., Balto‐Slavonic clade, Romano‐Germano‐Celtic clade, Armenian‐Greek group, and Indo‐Iranian group (the two last groups possibly paraphyletic); (b) the unstable position of the Albanian language; (c) the unstable pattern of the basalmost IE differentiation; but (d) the probable existence of the Balto‐Slavonic–Indo‐Iranian (“satem”) and the Romano‐Germano‐Celtic (+Albanian?) superclades. The results are compared with the phenetic approach to lexicostatistical data, the results of which are significantly less informative concerning the basal pattern. The results suggest a predominantly branching pattern of the basic vocabulary phylogeny and little borrowing of individual words. Different scenarios of IE differentiation based on archaeological and genetic information are discussed.     

Species and paleoanthropology

The biotic world is self-evidently “packaged” into units, of which the most basic is the species. It is necessary to develop an accurate understanding of what species are and how they are to be identified before we can proceed to more complex analyses of the evolutionary histories and relationships of extinct and extant taxa at all levels of the systematic hierarchy. In this article, we review the major species concepts current today among paleoanthropologists, and examine the limitations of their applicability to practical studies of extant and extinct faunas. The primary such limitation for paleoanthropologists is the fact that all major species definitions stress reproductive continuity (whether by exclusionary or inclusionary mechanisms), a quality that is inferential at best among forms known only as fossils (and, in many cases, in the extant fauna as well). The only reliable signal as to species status in the fossil record is morphology, yet speciation carries with it no specifiable quantity of morphological innovation. Some groups with autapomorphies are not species, and some species do not bear autapomorphies. How, then, are we to recognize species in the hominid and other fossil records? Noting that osteodental differences among congeneric primate species tend to be subtle, and that when consistent identifiable “morphs” can be found at least as many species are present, we recommend equating morphs based on several characters with species—realizing that only one or two distinctive characters may not make a morph. In this way, our views of the phylogenetic histories of higher taxa may be oversimplified, but their essential patterns will not be distorted.     

Multilocus ribosomal RNA phylogeny of the leaf beetles (Chrysomelidae)

Basal relationships in the Chrysomelidae (leaf beetles) were investigated using two nuclear (small and partial large subunits) and mitochondrial (partial large subunit) rRNA (≈ 3000 bp total) for 167 taxa covering most major lineages and relevant outgroups. Separate and combined data analyses were performed under parsimony and model‐based tree building algorithms from dynamic (direct optimization) and static (Clustal and BLAST) sequence alignments. The performance of methods differed widely and recovery of well established nodes was erratic, in particular when using single gene partitions, but showed a slight advantage for Bayesian inferences and one of the fast likelihood algorithms (PHYML) over others. Direct optimization greatly gained from simultaneous analysis and provided a valuable hypothesis of chrysomelid relationships. The BLAST‐based alignment, which removes poorly aligned sequence segments, in combination with likelihood and Bayesian analyses, resulted in highly defensible trees obtained in much shorter time than direct optimization, and hence is a viable alternative when data sets grow. The main taxonomic findings include the recognition of three major lineages of Chrysomelidae, including a basal “sagrine” clade (Criocerinae, Donaciinae, Bruchinae), which was sister to the “eumolpine” (Spilopyrinae, Eumolpinae, Cryptocephalinae, Cassidinae) plus “chrysomeline” (Chrysomelinae, Galerucinae) clades. The analyses support a broad definition of subfamilies (i.e., merging previously separated subfamilies) in the case of Cassidinae (cassidines + hispines) and Cryptocephalinae (chlamisines + cryptocephalines + clytrines), whereas two subfamilies, Chrysomelinae and Eumolpinae, were paraphyletic. The surprising separation of monocot feeding Cassidinae (associated with the eumolpine clade) from the other major monocot feeding groups in the sagrine clade was well supported. The study highlights the need for thorough taxon sampling, and reveals that morphological data affected by convergence had a great impact when combined with molecular data in previous phylogenetic analyses of Chrysomelidae. © The Willi Hennig Society 2007.     

Capuchin monkeys (Cebus apella) fail to show inequality aversion in a no-cost situation

Although humans show robust equality concerns across a variety of situations, there is ongoing debate regarding the extent to which any nonhuman species is inequality averse. In the current research, we test nonhuman primates' reactions to conspecifics receiving equal and unequal payoffs using a “no-cost” method in which subjects can respond to inequality without rejecting food. Specifically, we gave capuchin monkeys (Cebus apella) the opportunity to trade with one of two experimenters, each of whom offered the subject an identical reward, but had different histories of trading with the subject and a conspecific partner. An “equal” experimenter had previously given a conspecific the same reward that the subject had received, whereas the other experimenter was either an “advantageous trader” for the subject (giving the conspecific an inferior reward) or a “disadvantageous trader” for the subject (giving the conspecific a superior reward). By offering subjects a choice between experimenters, we removed several competing demands that may have masked the expression of robust equality preferences in previous studies. Even though there was no cost associated with expressing an equality preference, we found no evidence that capuchins differentiated between equal and unequal experimenters.     

Petite bodies of the “robust” australopithecines

The “robust” australopithecines are often depicted as having large and powerfully built bodies to match their massive masticatory apparatus, but until 1988 the sample of postcranial remains attributed with certainty to this group was very limited. Almost nothing was known about the body of the East African “robust” australopithecine because taxonomic attribution of the postcrania was so uncertain. The body of the South African “robust” australopithecine had to be reconstructed from about a dozen isolated fragments of postcrania. Now a partial skeleton is attributed with confidence to the East African “robust” group along with several isolated bones. The South African sample has more than tripled. Analyses of this vastly expanded sample reveal that a large portion of postcrania attributed to “robust” australopithecines from Swartkrans Member 1 (35%) are from extraordinarily small-bodied individuals similar in size to a modern Pygmy weighing as little as 28 kg. These small elements include parts from the forelimb, spine, and hindlimb. About 22% of these Swartkrans 1 “robust” australopithecines are about the same size as a modern human weighing about 43 kgs and about 43% are larger than this standard but less than or equal to a 54 kg modern human. Approximately the same pattern is true for the Swartkrans 2 hominids, but taxonomic attribution is less certain. All of the Member 3 specimens are similar in size to the 45 kg standard. The partial skeleton of the East African “robust” australopithecine (KNM-ER 1500) has hindlimb joints that would correspond to a modern human of 34 kgs although the actual weight may be 5 to 10 kgs greater judging from shaft robusticity and forelimb size. The largest postcranial element attributed with some certainty to the East African “robust” australopithecine group (the talus, KNM-ER 1464) is about the same overall size as a modern human of 54 kgs, although its tibial facet is slightly smaller. Although many previous studies have hinted at the possibility that “robust” australopithecines had relatively small bodies, the new fossils provide substantial evidence that these creatures ranged from quite small to only moderate in body size relative to modern humans. These were the petite-bodied vegetarian cousins of our ancestors. Sexual dimorphism in body size appears to be greater than that in modern humans, similar to that in Pan, and less than that in Gorilla or Pongo, although such comparisons are of limited value given the small samples, poorly known body proportions, time averaging, and many other problems.     

Plastomic data shed new light on the phylogeny,biogeography, and character evolution of the family Crassulaceae

Crassulaceae is a mid-sized family of angiosperms, most species of which are herbaceous succulents, usually with 5-merous flowers and one or two whorls of stamens. Although previous phylogenetic studies revealed seven major “clades” in Crassulaceae and greatly improved our understanding of the evolutionary history of the family, relationships among major clades are still contentious. In addition, the biogeographic origin and evolution of important morphological characters delimiting infrafamilial taxa have not been subject to formal biogeographic and character evolution analyses based on a well-supported phylogeny backbone. In this study, we used plastomic data of 52 species, representing all major clades revealed in previous studies to reconstruct a robust phylogeny of Crassulaceae, based on which we unraveled the spatiotemporal framework of diversification of the family. We found that the family may originate in southern Africa and then dispersed to the Mediterranean, from there to eastern Asia, Macaronesia, and North America. The crown age of Crassulaceae was dated at ca. 63.93 million years ago, shortly after the Cretaceous–Paleogene (K-Pg) boundary. We also traced the evolution of six important morphological characters previously used to delimit infrafamilial taxa and demonstrated widespread parallel and convergent evolution of both vegetative (life form and phyllotaxis) and floral characters (number of stamen whorls, petals free or fused, and flower merism). Our results provide a robust backbone phylogeny as a foundation for further investigations, and also some important new insights into biogeography and evolution of the family Crassulaceae.     

基于空间生态特性的景观图式语言研究方法与方法论

图式语言是基于景观空间的生态特性而建立的一种表达景观地方性和空间逻辑的新范式,是以图式为基本语言符号研究景观空间由基本空间、复合空间到整体景观空间的基本语汇与基本逻辑关系,并为塑造新景观提供语汇、语法等图式语言体系的支撑。图式语言研究是采用了景观空间原型与高效空间、空间选择与样本分析、空间抽象与图式提取、图式语汇与空间逻辑以及图式语言体系构建与验证的研究方法。图式语言的研究方法是基于结构主义与解构主义、自组织协同理论与逻辑设计、空间生成过程与空间推理以及景观的多重表意与语用学等方法论基础之上的。图式语言的研究方法和方法论基础是景观空间的系统性、有机性和演变性决定的,是多学科研究方法和方法论的综合。     

A novel multiple-site extension to pairwise partitioned taxonomic beta diversity

Our understanding of the causes of variation in taxonomic composition, or beta diversity, is progressing rapidly, thanks in part to recent methodological advances. For example, methods for partitioning beta diversity into its “replacement” and “richness” components have helped reveal patterns that had been undetected by traditional analyses. These partitioning methods are derived from pairwise dissimilarity measures, and are thus well suited to many conventional beta diversity analyses, including “distance decay” relationships. However, pairwise beta diversity measures have limitations, including their lack of information about taxa that are shared among three or more sites. Recently, a new suite of multiple-site counterparts to the pairwise partitioning measures of beta diversity was proposed, but the pairwise analogs upon which these were based were subsequently criticized, and compelling arguments were presented in favor of other partitioning approaches. Here, we introduce multiple-site partitioning measures that address these shortcomings, and illustrate their desirable properties using numerical simulations. We also provide an empirical example of their utility by analyzing the temporal beta diversity of breeding birds within the conterminous USA. We show that temporal beta diversity is predominantly driven by replacement rather than richness differences, and correspondingly, that correlations between temporal beta diversity and productivity and elevation are driven primarily by the replacement component. Furthermore, in contrast to existing multiple-site measures, we show that richness differences do play an important part in driving overall beta diversity patterns. Our new multiple-site measures therefore complement existing methods for analyzing beta diversity, and are especially suitable when compositional heterogeneity is the response of interest.     

Gardening for Homonyms: Integrating Science and Language Arts to Support Children's Creative Use of Multiple Meaning Words

Curriculum integration can increase the presence of science at the elementary level. The purpose of this article is to share how two second-grade teachers have integrated language arts content as a part of science-language arts instruction in a garden-based learning context. One application was a teacher-designed Gardening for Homonyms lesson, which supported new ways of thinking about words and wordplay while developing science vocabulary related to structure and function, diversity of life, and interdependent relationships in ecosystems. This article provides the lesson and discusses its implementation in two second-grade classrooms. Examples of student work illustrate children's creative thought around and application of multiple meaning words. Pre-, post-, and extended posttest measures of students' ability to generate and to use homonyms demonstrate that this science-language arts integrated lesson can result in both short- and long-term learning. Applications and follow-up from the lesson over two subsequent years have engaged second and third grade students in study/inquiry about plant growth and life cycles while utilizing many facets of language arts, which have ranged from labeling an experimental design and writing predictions and results to conversing about digital “GigaPan” images on growing strawberries.     

A phylogenetic approach to cultural evolution

There has been a rapid increase in the use of phylogenetic methods to study the evolution of languages and culture. Languages fit a tree model of evolution well, at least in their basic vocabulary, challenging the view that blending, or admixture among neighbouring groups, was predominant in cultural history. Here, we argue that we can use language trees to test hypotheses about not only cultural history and diversification, but also bio-cultural adaptation. Phylogenetic comparative methods take account of the non-independence of cultures (Galton's problem), which can cause spurious statistical associations in comparative analyses. Advances in phylogenetic methods offer new possibilities for the analysis of cultural evolution, including estimating the rate of evolution and the direction of coevolutionary change of traits on the tree. They also enable phylogenetic uncertainty to be incorporated into the analyses, so that one does not have to treat phylogenetic trees as if they were known without error.     

The natural history of verb-stem reduplication in Bantu

In this study I present a comparative and historical analysis of “frequentative” Bantu verb-stem reduplication, many of whose variants have been described for a number of Eastern and Southern Bantu languages. While some languages have full-stem compounding, where the stem consists of the verb root plus any and all suffixes, others restrict the reduplicant to two syllables. Two questions are addressed: (i) What was the original nature of reduplication in Proto-Bantu? (ii) What diachronic processes have led to the observed variation? I first consider evidence that the frequentative began as full-stem reduplication, which then became restricted either morphologically (by excluding inflectional and ultimately derivational suffixes) and/or phonologically (by imposing a bisyllabic maximum size constraint). I then turn to the opposite hypothesis and consider evidence and motivations for a conflicting tendency to rebuild full-stem reduplication from the partial reduplicant. I end by attempting to explain why the partial reduplicant is almost always preposed to the fuller base.     

“Active” and “passive” ecological restoration strategies in meta‐analysis

One of the means of creating a more robust methodology for ecological restoration involves reducing the gap between ecological theory and restoration practices. A common strategy to do so is using meta‐analysis to understand key drivers of restoration outcomes. “Active” and “passive” is a dichotomy often used to separate restoration strategies in such meta‐analyses. We investigate previously raised concerns about selection bias and subjective categorization of strategies. We promote a paired experimental design in future empirical research and propose the use of three categories of restoration strategy in lieu of “passive” and “active” to alleviate inconsistency in definitions and categorization.     

Unraveling the evolutionary history of the nematode Pristionchus pacificus: from lineage diversification to island colonization

The hermaphroditic nematode Pristionchus pacificus is a model organism with a range of fully developed genetic tools. The species is globally widespread and highly diverse genetically, consisting of four major independent lineages (lineages A, B, C, and D). Despite its young age (~2.1 Ma), volcanic La Réunion Island harbors all four lineages. Ecological and population genetic research studies suggest that this diversity is due to repeated independent island colonizations by P. pacificus. Here, we use model‐based statistical methods to rigorously test hypotheses regarding the evolutionary history of P. pacificus. First, we employ divergence analyses to date diversification events among the four “world” lineages. Next, we examine demographic properties of a subset of four populations (“a”, “b”, “c”, and “d”), present on La Réunion Island. Finally, we use the results of the divergence and demographic analyses to inform a modeling‐based approximate Bayesian computation (ABC) approach, where we test hypotheses about the order and timing of establishment of the Réunion populations. Our dating estimates place the recent common ancestor of P. pacificus lineages at nearly 500,000 generations past. Our demographic analysis supports recent (<150,000 generations) spatial expansion for the island populations, and our ABC approach supports c>a>b>d as the most likely colonization order of the island populations. Collectively, our study comprehensively improves previous inferences about the evolutionary history of P. pacificus.